Exhibit 31.1

CERTIFICATION

I, Robert M. Thornton, Jr., the
Chief Executive Officer of SunLink Health Systems, Inc. (the Company), certify that:

(1) I have reviewed this
quarterly report on Form 10-Q of the Company for the period ended December 31, 2009 (the Report);

(2) Based
on my knowledge, this Report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with
respect to the period covered by this Report;

(3) Based on my knowledge, the financial statements and other financial
information included in this Report fairly present in all material respects the financial condition, results of operations and cash flows of the Company as of, and for, the periods presented in this Report;

(4) The Companys other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as
defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for the Company and have:

(a) Designed such disclosure controls and
procedures or caused such disclosure controls and procedures to be designed under our supervision to ensure that material information relating to the Company, including its consolidated subsidiaries, is made known to us by others within those
entities, particularly during the period in which this Report is being prepared;

(b) {Intentionally Omitted in reliance on SEC
Release No. 33-8238; 34-47986, Section III.E.};

(c) Evaluated the effectiveness of the Companys disclosure controls
and procedures and presented in this Report our conclusions about the effectiveness of the disclosure controls and procedures, as of December 31, 2009 (the Evaluation Date), based on such evaluation; and

(d) Disclosed in this Report any change in the Companys internal control over financial reporting that occurred during the
Companys most recent fiscal quarter ended on the Evaluation Date that has materially affected, or is reasonably likely to materially affect, the Companys internal control over financial reporting; and

(5) The Companys other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial
reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)), to the Companys auditors and the audit committee of the Companys board of directors (or persons performing the equivalent functions):

(a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are
reasonably likely to adversely affect the Companys ability to record, process, summarize and report financial information; and

(b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the Companys internal control over financial reporting.



|                  |  |  |  |                             
|----------------- |  |  |  | ----------------------------
|                  |  | 
|February 11, 2010 |  |  |  | /s/ Robert M. Thornton, Jr. 
|                  |  |  |  | Robert M. Thornton, Jr.     
|                  |  |  |  | SunLink Health Systems, Inc.
|                  |  |  |  | Chief Executive Officer